Changes between Initial Version and Version 2 of Ticket #20746


Ignore:
Timestamp:
Jul 13, 2026, 4:09:26 PM (43 hours ago)
Author:
Greg Couch
Comment:

I've changed the daily build to delay adding the metal bonds until after the small molecule is connected by distance. Please try tomorrow's daily build and let me that does what you expect.

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  • Ticket #20746

    • Property Component Unassigned → Input/Output
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → feedback
    • Property Summary ChimeraX bug report submission → Corecif has metal coordination bonds only

  • Ticket #20746 – Description

    initial v2  
    33Platform:        Windows-10-10.0.26200
    44ChimeraX Version: 1.13.dev202606240437 (2026-06-24 04:37:46 UTC)
     5}}}
    56Description
     7
    68Picked up a new pathological case for `corecif`: for reasons known only to them, it's common for authors of organometallic crystal structures to *only* report the metal coordination bonds, not the covalent ones. This breaks `corecif`'s geometry-based bonding perception - it skips adding new bonds for any atom that already has a bond defined in the cif, and metal-coordination bonds apparently count for that test. So every organic ligand in close contact with a metal ends up as just a point cloud of atoms.
    7 
     9{{{
    810Log:
    911> clipper init